Modern approaches to therapeutic oligonucleotide manufacturing.

Therapeutic oligonucleotides are a powerful drug modality with the potential to treat many diseases. The rapidly growing number of therapies that have been approved and that are in advanced clinical trials will place unprecedented demands on our capacity to manufacture oligonucleotides at scale. Existing methods based on solid-phase phosphoramidite chemistry are limited by their scalability and sustainability, and new approaches are urgently needed to deliver the multiton quantities of oligonucleotides that are required for therapeutic applications. The chemistry community has risen to the challenge by rethinking strategies for oligonucleotide production. Advances in chemical synthesis, biocatalysis, and process engineering technologies are leading to increasingly efficient and selective routes to oligonucleotide sequences. We review these developments, along with remaining challenges and opportunities for innovations that will allow the sustainable manufacture of diverse oligonucleotide products.

Propagation-based x-ray phase-contrast tomography of mastectomy samples using synchrotron radiation.

PURPOSE: Propagation-based phase-contrast computed tomography (PB-CT) is a method for three-dimensional x-ray imaging that utilizes refraction, as well as absorption, of x rays in the tissues to increase the signal-to-noise ratio (SNR) in the resultant images, in comparison with equivalent conventional absorption-only x-ray tomography (CT). Importantly, the higher SNR is achieved without sacrificing spatial resolution or increasing the radiation dose delivered to the imaged tissues. The present work has been carried out in the context of the current development of a breast CT imaging facility at the Australian Synchrotron. METHODS: Seven unfixed complete mastectomy samples with and without breast cancer lesions have been imaged using absorption-only CT and PB-CT techniques under controlled experimental conditions. The radiation doses delivered to the mastectomy samples during the scans were comparable to those approved for mammographic screening. Physical characteristics of the reconstructed images, such as spatial resolution and SNR, have been measured and compared with the results of the radiological quality assessment of the complete absorption CT and PB-CT image stacks. RESULTS: Despite the presence of some image artefacts, the PB-CT images have outperformed comparable absorption CT images collected at the same radiation dose, in terms of both the measured objective image characteristics and the radiological image scores. The outcomes of these experiments are shown to be consistent with predictions of the theory of PB-CT imaging and previous reported experimental studies of this imaging modality. CONCLUSIONS: The results presented in this paper demonstrate that PB-CT holds a high potential for improving on the quality and diagnostic value of images obtained using existing medical x-ray technologies, such as mammography and digital breast tomosynthesis (DBT). If implemented at suitable synchrotron imaging facilities, PB-CT can be used to complement existing imaging modalities, leading to more accurate breast cancer diagnosis.

Free propagation phase-contrast breast CT provides higher image quality than cone-beam breast-CT at low radiation doses: a feasibility study on human mastectomies.

In this study we demonstrate the first direct comparison between synchrotron x-ray propagation-based CT (PB-CT) and cone-beam breast-CT (CB-CT) on human mastectomy specimens (N = 12) including different benign and malignant lesions. The image quality and diagnostic power of the obtained data sets were compared and judged by two independent expert radiologists. Two cases are presented in detail in this paper including a comparison with the corresponding histological evaluation. Results indicate that with PB-CT it is possible to increase the level of contrast-to-noise ratio (CNR) keeping the same level of dose used for the CB-CT or achieve the same level of CNR reached by CB-CT at a lower level of dose. In other words, PB-CT can achieve a higher diagnostic potential compared to the commercial breast-CT system while also delivering a considerably lower mean glandular dose. Therefore, we believe that PB-CT technique, if translated to a clinical setting, could have a significant impact in improving breast cancer diagnosis.

Association between the oxidative status, Vitamin D levels and respiratory function in asthmatic children.

AIM: We studied the relationship between plasma concentrations of oxidative system markers, vitamin D, and respiratory functions in children with asthma. MATERIALS AND METHODS: Ninety one children aged 6-17 years with stable asthma seen in the clinic had the serum concentrations of oxidative system markers [total antioxidant capacity (TAC), total oxidative status (TOS), paraoxonase-1 activity (PON-1), and 25-hydroxyvitamin D3] and respiratory functions were measured. RESULTS: There was no statistical correlation between TAC and age and FEV1. There was a significant positive correlation between TAC and 25(OH)D3 (r = 0.214, P = 0.021), TAC and TOS (r = 0.218, P = 0.007), TAC and PON-1 (r = 0.230, P = 0.028), TAC and IgE (r = 0.194, P = 0.033), and inverse correlation between TAC and PEF (r = -0.208, P = 0.024). In the backward multiple regression analysis, 25(OH)D3 (t = 2.613, P = 0.011), age (t = -2.158, P = 0.034), TOS (t = 2.158, P = 0.000), and OSI index (t = -13.859 P = 0.000) maintained an independent relationship with TAC (r = 0.858, r2 = 0.737, F = 21.436, P = 0.000). CONCLUSION: Oxidative stress correlates with the serum vitamin D concentrations. Clinical trials are required to confirm that increasing serum 25OHD may improve asthma control, as measured by clinical and oxidative stress markers.

Optimization of propagation-based x-ray phase-contrast tomography for breast cancer imaging.

The aim of this study was to optimise the experimental protocol and data analysis for in-vivo breast cancer x-ray imaging. Results are presented of the experiment at the SYRMEP beamline of Elettra Synchrotron using the propagation-based phase-contrast mammographic tomography method, which incorporates not only absorption, but also x-ray phase information. In this study the images of breast tissue samples, of a size corresponding to a full human breast, with radiologically acceptable x-ray doses were obtained, and the degree of improvement of the image quality (from the diagnostic point of view) achievable using propagation-based phase-contrast image acquisition protocols with proper incorporation of x-ray phase retrieval into the reconstruction pipeline was investigated. Parameters such as the x-ray energy, sample-to-detector distance and data processing methods were tested, evaluated and optimized with respect to the estimated diagnostic value using a mastectomy sample with a malignant lesion. The results of quantitative evaluation of images were obtained by means of radiological assessment carried out by 13 experienced specialists. A comparative analysis was performed between the x-ray and the histological images of the specimen. The results of the analysis indicate that, within the investigated range of parameters, both the objective image quality characteristics and the subjective radiological scores of propagation-based phase-contrast images of breast tissues monotonically increase with the strength of phase contrast which in turn is directly proportional to the product of the radiation wavelength and the sample-to-detector distance. The outcomes of this study serve to define the practical imaging conditions and the CT reconstruction procedures appropriate for low-dose phase-contrast mammographic imaging of live patients at specially designed synchrotron beamlines.

The compromise of dynamic disulfide/thiol homeostasis as a biomarker of oxidative stress in trichloroethylene exposure.

In this study, we aimed to investigate disulfide/thiol homeostasis in trichloroethylene (TCE) exposure. The study was carried out in 30 nonsmoker TCE-exposed workers with a variety of occupations. Additionally, 30 healthy nonsmoker volunteers were recruited as the control group. TCE exposure was determined by measuring urinary trichloroacetic acid (TCA) concentration. Median urinary TCA levels of exposed workers (20.5 mg/L) were significantly higher than control subjects (5 mg/L). Thiol and disulfide concentrations were determined using a novel automated method. Disulfide/thiol ratio was significantly higher in the exposed group (p < 0.001). Thiol/disulfide homeostasis was found to be disturbed in TCE-exposed workers. We predict that in TCE-exposed workers this disturbance can be a therapeutic target, and the efficiency of the treatment can easily be monitored by the novel method we used.

Aqueous V(V)-peroxo-amino acid chemistry. Synthesis, structural and spectroscopic characterization of unusual ternary dinuclear tetraperoxo vanadium(V)-glycine complexes.

Vanadium participation in cellular events entails in-depth comprehension of its soluble and bioavailable forms bearing physiological ligands in aqueous distributions of binary and ternary systems. Poised to understand the ternary V(V)-H(2)O(2)-amino acid interactions relevant to that metal ion's biological role, we have launched synthetic efforts involving the physiological ligands glycine and H(2)O(2). In a pH-specific fashion, V(2)O(5), glycine, and H(2)O(2) reacted and afforded the unusual complexes (H(3)O)(2)[V(2)(O)(2)(mu(2):eta(2):eta(1)-O(2))(2)(eta(2)-O(2))(2)(C(2)H(5)NO(2))] x 5/4 H(2)O (1) and K(2)[V(2)(O)(2)(mu(2):eta(2):eta(1)-O(2))(2)(eta(2)-O(2))(2)(C(2)H(5)NO(2))] x H(2)O (2). 1 crystallizes in the triclinic space group P1, with a = 7.805(4) A, b = 8.134(5) A, c = 12.010(7) A, alpha = 72.298(9) degrees, beta = 72.991(9) degrees, gamma = 64.111(9) degrees, V = 641.9(6) A(3), and Z = 2. 2 crystallizes in the triclinic space group P1, with a = 7.6766(9) A, b = 7.9534(9) A, c = 11.7494(13) A, alpha = 71.768(2) degrees, beta = 73.233(2) degrees, gamma = 65.660(2) degrees, V = 610.15(12) A(3), and Z = 2. Both complexes 1 and 2 were characterized by UV/visible, LC-MS, FT-IR, Raman, NMR spectroscopy, cyclic voltammetry, and X-ray crystallography. The structures of 1 and 2 reveal the presence of unusual ternary dinuclear vanadium-tetraperoxo-glycine complexes containing [(V(V)=O)(O(2))(2)](-) units interacting through long V-O bonds and an effective glycinate bridge. The latter ligand is present in the dianionic assembly as a bidentate moiety spanning both V(V) centers in a zwitterionic form. The collective physicochemical properties of the two ternary species 1 and 2 project the chemical role of the low molecular mass biosubstrate glycine in binding V(V)-diperoxo units, thereby stabilizing a dinuclear V(V)-tetraperoxo dianion. Structural comparisons of the anions in 1 and 2 with other known dinuclear V(V)-tetraperoxo binary anionic species provide insight into the chemical reactivity of V(V)-diperoxo species in key cellular events such as insulin mimesis and antitumorigenicity, potentially modulated by the presence of glycinate and hydrogen peroxide.

Novel chemistry of alpha-tosyloxy ketones: applications to the solution- and solid-phase synthesis of privileged heterocycle and enediyne libraries.

New synthetic technologies for the preparation and elaboration of alpha-tosyloxy ketones in solution- and on solid-phase are described. Both olefins and ketones serve as precursors to these relatively stable chemical entities: olefins via a novel one-pot epoxidation, arylsulfonic acid displacement, and oxidation sequence, and ketones by direct exposure to arylsulfonic acids in the presence of diacetoxy iodobenzene. Reaction of these substrates with O-, S-, or N-centered nucleophiles leads to incorporation of the nucleophile with concomitant expulsion of the sulfonate, while exposure to bis-functional nucleophiles furnishes annulated heterocyclic systems. In addition, the reactions of carbon-centered nucleophiles with alpha-tosylyloxy ketones are also explored. The collated data for all these nucleophiles provide compelling evidence for the proposal that different reaction pathways are followed when alpha-tosyloxy ketones are engaged by "hard" versus "soft" nucleophiles. The accessibility and site-selectivity of the chemistry demonstrated herein offer the promise of an expanded use for this moiety in solid-phase library construction, in particular, and in the field of organic synthesis, in general.

Total synthesis of the CP-molecules (CP-263,114 and CP-225,917, phomoidrides B and A). 1. Racemic and asymmetric synthesis of bicyclo[4.3.1] key building blocks.

A brief introduction into the chemistry of the CP-molecules is followed by first-generation synthetic sequences toward key building blocks for their total synthesis. Processes for both racemic and enantiomerically enriched bicyclo[4.3.1] ketone 6 or its equivalent are described, and the absolute stereochemistries of the optically enriched intermediates are determined. The efficient route developed to racemic 6 and the ready access to both enantiomers of key building blocks provided the opportunity for the total synthesis of the CP-molecules and determination of their absolute stereochemistry.

Total synthesis of the CP-molecules (CP-263,114 and CP-225,917, phomoidrides B and A). 2. Model studies for the construction of key structural elements and first-generation strategy.

Crucial model synthetic and mechanistic studies directed toward the development of methodology for the construction of the maleic anhydride moiety of the CP-molecules are described. Studies directed toward the stereoselective attachment of the upper side chain, culminating in the discovery of long-range stereochemical control, are also discussed. In addition, a first-generation strategy toward the CP-molecules, establishing key intermediate 5 as a "beachhead" from which all future operations would diverge, is also presented. Although this first-generation strategy failed to yield the target molecules, the endeavor laid the important groundwork for the next-generation drives toward the CP-molecules.

Total synthesis of the CP-molecules (CP-263,114 and CP-225,917, phomoidrides B and A). 3. Completion and synthesis of advanced analogues.

The completion of the total syntheses of the CP-molecules is reported. Several strategies and tactics, including the use of amide-based protecting groups for the homologated C-29 carboxylic acid and the use of an internal pyran protecting group scheme, are discussed. The endeavors leading to the design of new methods for the homologation of hindered aldehydes and to the isolation of a polycyclic byproduct (23), which inspired the development of a new series of reactions based on iodine(V) reagents, are described. In addition, the discovery and development of the LiOH-mediated conversion of CP-263,114 (1) to CP-225,917 (2) is described, and a mechanistic rationale is presented. Finally, a synthetic route to complex analogues of the CP-molecules harboring a maleimide moiety in place of the maleic anhydride is presented.

Iodine(V) reagents in organic synthesis. Part 1. Synthesis of polycyclic heterocycles via Dess-Martin periodinane-mediated cascade cyclization: generality, scope, and mechanism of the reaction.

The scope, generality, and mechanism of the Dess-Martin periodinane-mediated cyclization reaction of unsaturated anilides discovered during the total synthesis of the CP-molecules (phomoidrides A and B) are delineated. A plethora of heterocyclic compounds are accessible by employing gamma,delta-unsaturated amides (derived from anilines and carboxylic acids), urethanes, or ureas (derived from isocyanates and allylic alcohols and amines) as substrates. Optimization of the reaction led to room-temperature conditions, while isotope labeling studies allowed a mechanistic rationale for this cascade reaction.

Iodine(V) reagents in organic synthesis. Part 2. Access to complex molecular architectures via Dess-Martin periodinane-generated o-imidoquinones.

o-Imidoquinones, a rather rare class of compounds, are prepared from anilides by the action of Dess-Martin periodinane (DMP) and water. Their chemistry has been extensively investigated and found to lead to p-quinones and polycyclic systems of diverse molecular architectures. Applications of this methodology to the total synthesis of the naturally occurring compounds, epoxyquinomycin B and BE-10988, are described. Finally, another rare chemical entity, the ketohydroxyamide moiety, has been accessed through this DMP-based synthetic technology, and its reactivity has been studied. Among its most useful reactions is a set of cascade heterocyclic annulations leading to a variety of polycyclic systems of possible biological relevance.

Iodine(V) reagents in organic synthesis. Part 4. o-Iodoxybenzoic acid as a chemospecific tool for single electron transfer-based oxidation processes.

o-Iodoxybenzoic acid (IBX), a readily available hypervalent iodine(V) reagent, was found to be highly effective in carrying out oxidations adjacent to carbonyl functionalities (to form alpha,beta-unsaturated carbonyl compounds) and at benzylic and related carbon centers (to form conjugated aromatic carbonyl systems). Mechanistic investigations led to the conclusion that these new reactions are initiated by single electron transfer (SET) from the substrate to IBX to form a radical cation which reacts further to give the final products. Fine-tuning of the reaction conditions allowed remarkably selective transformations within multifunctional substrates, elevating the status of this reagent to that of a highly useful and chemoselective oxidant.

Iodine(V) reagents in organic synthesis. Part 3. New routes to heterocyclic compounds via o-iodoxybenzoic acid-mediated cyclizations: generality, scope, and mechanism.

The discovery and development of the o-iodoxybenzoic acid (IBX) reaction with certain unsaturated N-aryl amides (anilides) to form heterocycles are described. The application of the method to the synthesis of delta-lactams, cyclic urethanes, hydroxy amines, and amino sugars among other important building blocks and intermediates is detailed. In addition to the generality and scope of this cyclization reaction, this article describes a number of mechanistic investigations suggesting a single electron transfer from the anilide functionality to IBX and implicating a radical-based mechanism for the reaction.

Synthetic approaches to a variety of covalently linked porphyrin--fullerene hybrids.

There is substantial interest in dyads in which C(60) is covalently linked to electron donors, such as porphyrins, which absorb light strongly in the visible region. We present here the details of the syntheses of such compounds, which can be broadly organized into categories depending upon the nature of the linker joining the two chromophores. The structural aspects of intramolecular electronic interaction that we have sought to explore have dictated the synthetic strategies employed to generate these classes of molecules. Flexible glycol linkers were used to allow close approach between the fullerene and porphyrin, facilitating through-space interactions. These linkers also allowed studies of the effects of metal cation complexation. Naphthalene and alkyne linkers were used to examine the possible effects a conjugated or aromatic linker might have on photophysical properties. Finally, steroids were used as linkers in dyads expected to possess a large distance between the two chromophores, in which only through-bond interactions between the fullerene and porphyrin should be possible.

Selective imidazolidine ring opening during complex formation of iron(III), copper(II), and zinc(II) with a multidentate ligand obtained from 2-pyridinecarboxaldehyde N-oxide and triethylenetetramine.

The condensation of 2-pyridinecarboxaldehyde N-oxide and triethylenetetramine yields a product with two imidazolidine rings, as proven by a solid-state X-ray structure analysis as well as by NMR solution spectra. This ligand, L1, undergoes a ring-opening reaction on complex formation with Cu(II), yielding [CuL2]2+ where L2 functions as a pentadentate ligand, containing only one imidazolidine ring. On complexation with Zn(II) and Fe(III), both rings are opened and the complexes [ZnL3]2+ and [FeL3]3+ with a hexadentate L3 ligand are formed. The recrystallization of [ZnL3]2+ from DMSO solution results in the complex [ZnL1(DMSO)2]2+ in which L1 behaves as a tetradentate ligand. Thus L1, L2, and L3 are structural isomers with two, one, or no imidazolidine rings, as confirmed by X-ray structure analyses. The intramolecular ring formation is the result of the nucleophilic addition of the N(amino) group to the electrophilic sp2-hybridized -HC delta+=N site. Owing to the absence of the chelate effect on the sp3-hybridized carbon atom belonging to the imidazolidine ring, the ring opening is facilitated and readily observed upon complex formation with Cu(II), Zn(II), and Fe(III).

Novel strategies to construct the gamma-hydroxy lactone moiety of the CP molecules. Synthesis of the CP-225,917 core skeleton.

[formula: see text] The array of challenging structural lineaments embodied in the CP molecules (1 and 2, Figure 1) offers synthetic chemists uncharted realms of exploration and discovery. In this communication, we focus on the chemical hurdies posed by the gamma-hydroxy lactone moiety of these exciting targets. Thus, the examination of the general reactivity of these systems, the development of a novel tandem oxidation sequence to construct the gamma-hydroxy lactone moiety, and the successful construction of the complete polycyclic core of 2 (compound 28, Scheme 5) is enumerated within.